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bioRxiv (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.

Articles are not peer-reviewed, edited, or typeset before being posted online. However, all articles undergo a basic screening process for offensive and/or non-scientific content. No endorsement of an article’s methods, assumptions, conclusions, or scientific quality by Cold Spring Harbor Laboratory is implied by its appearance in bioRxiv. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published.

Authors may submit a revised version of an article to bioRxiv at any time. Once posted on bioRxiv, articles are citable and therefore cannot be removed.


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by Thomas F. Willems; Melissa Gymrek; Gareth Highnam; - The 1000 Genomes Project; David Mittelman; Yaniv Erlich
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Short Tandem Repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across over 1,000...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/07/10/004671
biorxiv
by Keisha Dawn Carlson; Peter H Sudmant; Maximilian Oliver Press; Evan E Eichler; Jay Shendure; Christine Queitsch
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Abstract Short tandem repeats (STRs) are highly mutable genetic elements that often reside in functional genomic regions. The cumulative evidence of genetic studies on individual STRs suggests that STR variation profoundly affects phenotype and contributes to trait heritability. Despite recent advances in sequencing technology, STR variation has remained largely inaccessible across many individuals compared to single nucleotide variation or copy number variation. STR genotyping with short-read...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/07/28/007500
biorxiv
by Iosif Lazaridis; Nick Patterson; Alissa Mittnik; Gabriel Renaud; Swapan Mallick; Karola Kirsanow; Peter H. Sudmant; Joshua G. Schraiber; Sergi Castellano; Mark Lipson; Bonnie Berger; Tatijana Zemunik; Alan Cooper; Cristian Capelli; Mark G. Thomas; Andres Ruiz-Linares; Sarah A. Tishkoff; Lalji Singh; Kumarasamy Thangaraj; Richard Villems; David Comas; Christos Economou; Rem Sukernik; Mait Metspalu; Matthias Meyer; Evan E. Eichler; Joachim Burger; Montgomery Slatkin; Svante Pååbo; Janet Kelso; David Reich; Johannes Krause; Ruth Bollongino; Qiaomei Fu; Kirsten Bos; Susanne Nordenfelt; Heng Li; Cesare de Filippo; Kay Prüfer; Susanna Sawyer; Cosimo Posth; Wolfgang Haak; Fredrik Hallgren; Elin Fornander; Nadin Rohland; Dominique Delsate; Michael Francken; Jean-Michel Guinet; Joachim Wahl; George Ayodo; Hamza A. Babiker; Graciela Baillet; Elena Balanovska; Oleg Balanovsky; Ramiro Barrantes; Gabriel Bedoya; Haim Ben-Ami; Judit Bene; Fouad Berrada; Claudio M. Bravi; Francesca Brisighelli; George B.J. Busby; Francesco Cali; Mikhail Churnosov; David E.C. Cole; Daniel Corach; Larissa Damba; George van Driem; Stanislav Dryomov; Jean-Michel Dugoujon; Sardana A. Fedorova; Irene Gallego Romero; Marina Gubina; Michael Hammer; Brenna Henn; Tor Helvig; Ugur Hodoglugil; Aashish R. Jha; Sena Karachanak-Yankova; Rita Khusainova; Elza Khusnutdinova; Rick Kittles; Toomas Kivisild; William Klitz; Vaidutis Kučinskas; Alena Kushniarevich; Leila Laredj; Sergey Litvinov; Theologos Loukidis; Robert W. Mahley; Béla Melegh; Ene Metspalu; Julio Molina; Joanna Mountain; Klemetti Näkkäläjärvi; Desislava Nesheva; Thomas Nyambo; Ludmila Osipova; Jüri Parik; Fedor Platonov; Olga L. Posukh; Valentino Romano; Francisco Rothhammer; Igor Rudan; Ruslan Ruizbakiev; Hovhannes Sahakyan; Antti Sajantila; Antonio Salas; Elena B. Starikovskaya; Ayele Tarekegn; Draga Toncheva; Shahlo Turdikulova; Ingrida Uktveryte; Olga Utevska; René Vasquez; Mercedes Villena; Mikhail Voevoda; Cheryl Winkler; Levon Yepiskoposyan; Pierre Zalloua
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We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/04/05/001552
biorxiv
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Summary: Genome-wide association studies (GWAS) have identified thousands of human trait-associated single nucleotide polymorphisms. Here, I describe a freely available R package for visualizing GWAS results using Q-Q and manhattan plots. The qqman package enables the flexible creation of manhattan plots, both genome-wide and for single chromosomes, with optional highlighting of SNPs of interest. Availability: qqman is released under the GNU General Public License, and is freely available on...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/05/14/005165
biorxiv
by Irene Gallego Romero; Bryan J Pavlovic; Irene Hernando-Herraez; Nicholas E Banovich; Courtney L Kagan; Jonathan E Burnett; Constance H Huang; Amy Mitrano; Claudia I Chavarria; Inbar F Ben-Nun; Yingchun Li; Karen Sabatini; Trevor R Leonardo; Mana Parast; Tomas Marques-Bonet; Louise C Laurent; Jeanne F Loring; Yoav Gilad
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Comparative genomics studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/09/06/008862.1
biorxiv
by Neville E Sanjana; Ophir Shalem; Feng Zhang
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Genome-wide, targeted loss-of-function pooled screens using the CRISPR (clustered regularly interspaced short palindrome repeats)?associated nuclease Cas9 in human and mouse cells provide an alternative screening system to RNA interference (RNAi). Initial lentiviral delivery systems for CRISPR screening had low viral titer or required a cell line already expressing Cas9, limiting the range of biological systems amenable to screening. In this work, we present 1- and 2-vector lentiCRISPR systems...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/06/28/006726
biorxiv
by John G Cleary; Ross Braithwaite; Kurt Gaastra; Brian S Hilbush; Stuart Inglis; Sean A Irvine; Alan Jackson; Richard Littin; Sahar Nohzadeh-Malakshah; Minita Shah; Mehul Rathod; David Ware; Len Trigg; Francisco M De La Vega
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The analysis of whole-genome or exome sequencing data from trios and pedigrees has being successfully applied to the identification of disease-causing mutations. However, most methods used to identify and genotype genetic variants from next-generation sequencing data ignore the relationships between samples, resulting in significant Mendelian errors, false positives and negatives. Here we present a Bayesian network framework that jointly analyses data from all members of a pedigree...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/01/24/001958
biorxiv
by Ashley P Ng; Maria Kauppi; Donald Metcalf; Craig D Hyland; Emma C Josefsson; Marion Lebois; Jian-Guo Zhang; Ladina Di Rago; Tracey Baldwin; Douglas J Hilton; Warren S Alexander
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Thrombopoietin (TPO) acting via its receptor Mpl is the major cytokine regulator of platelet number. To precisely define the role of specific hematopoietic cells in TPO dependent hematopoiesis, we generated mice that express the Mpl receptor normally on stem/progenitor cells but lack expression on megakaryocytes and platelets ( MplPF4cre/PF4cre . MplPF4cre/PF4cre mice displayed profound megakaryocytosis and thrombocytosis with a remarkable expansion of megakaryocyte-committed and multipotential...
Topic: Cell Biology
Source: http://biorxiv.org/content/early/2014/03/19/003459
biorxiv
by Akihiro Shimokawa; Yuki Tonooka; Misato Matsumoto; Hironori Ara; Hiroshi Suzuki; Naoki Yamauchi; Masayoshi Shigyo
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Because global climate change has made agricultural supply unstable, plant factories are expected to be a safe and stable means of food production. As the light source of a plant factory or controlled greenhouse, the light emitting diode (LED) is expected to solve cost problems and promote plant growth efficiently. In this study, we examined the light condition created by using monochromatic red and blue LEDs, to provide both simultaneous and alternating irradiation to leaf lettuce. The result...
Topic: Plant Biology
Source: http://biorxiv.org/content/early/2014/02/28/003103
biorxiv
by Magali Soumillon; Davide Cacchiarelli; Stefan Semrau; Alexander van Oudenaarden; Tarjei S Mikkelsen
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Directed differentiation of cells in vitro is a powerful approach for dissection of developmental pathways, disease modeling and regenerative medicine, but analysis of such systems is complicated by heterogeneous and asynchronous cellular responses to differentiation-inducing stimuli. To enable deep characterization of heterogeneous cell populations, we developed an efficient digital gene expression profiling protocol that enables surveying of mRNA in thousands of single cells at a time. We...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/03/05/003236
biorxiv
by Fillip Port; Hui-Min Chen; Tzumin Lee; Simon L Bullock
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The type II CRISPR/Cas system has recently emerged as a powerful method to manipulate the genomes of various organisms. Here, we report a novel toolbox for high efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germline restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/03/26/003541
biorxiv
by Anna Szécsényi-Nagy; Guido Brandt; Victoria Keerl; János Jakucs; Wolfgang Haak; Sabine Möller-Rieker; Kitti Köhler; Balázs Mende; Marc Fecher; Krisztián Oross; Tibor Paluch; Anett Osztás; Viktória Kiss; György Pálfi; Erika Molnár; Katalin Sebők; András Czene; Tibor Paluch; Mario Šlaus; Mario Novak; Nives Pećina-Šlaus; Brigitta Ősz; Vanda Voicsek; Krisztina Somogyi; Gábor Tóth; Bernd Kromer; Eszter Bánffy; Kurt Alt
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Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/09/03/008664
biorxiv
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The debate over the ethnogenesis of Ashkenazi Jewry is longstanding, and has been hampered by a lack of Jewish historiographical work between the Biblical and the early Modern eras. Most historians, as well as geneticists, situate them as the descendants of Israelite tribes whose presence in Europe is owed to deportations during the Roman conquest of Palestine, as well as migration from Babylonia, and eventual settlement along the Rhine. By contrast, a few historians and other writers, most...
Topic: Genetics
Source: http://biorxiv.org/content/early/2013/12/12/001354
biorxiv
by Sebastian Gil Anthony Konietzny; Phillip Byron Pope; Aaron Weimann; Alice Carolyn McHardy
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Background: Efficient industrial processes for converting plant lignocellulosic materials into biofuels are a key challenge in global efforts to use alternative energy sources to fossil fuels. Novel cellulolytic enzymes have been discovered from microbial genomes and metagenomes of microbial communities. However, the identification of relevant genes without known homologs, and elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain a challenge....
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/05/21/005355
biorxiv
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Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Because they are small, they can escape filtration in culture media. Because they lack cell walls, they are resistant to commonly used antibiotics. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/07/11/007054
biorxiv
by Castle Raley; David Munroe; Kristie Jones; Yu-Chih Tsai; Yan Guo; Bao Tran; Sujatha Gowda; Jennifer L. Troyer; Daniel R. Soppet; Claudia Stewart; Robert Stephens; Jack Chen; TF Skelly; Cheryl Heiner; Jonas Korlach; Dwight Nissley
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We have developed and validated an amplification-free method for generating DNA sequencing libraries from very low amounts of input DNA (500 picograms - 20 nanograms) for single-molecule sequencing on the Pacific Biosciences (PacBio) RS II sequencer. The common challenge of high input requirements for single-molecule sequencing is overcome by using a carrier DNA in conjunction with optimized sequencing preparation conditions and re-use of the MagBead-bound complex. Here we describe how this...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/03/25/003566
biorxiv
by Krzysztof M Kozak; Niklas Wahlberg; Andrew Neild; Kanchon K Dasmahapatra; James Mallet; Chris D Jiggins
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Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, and is associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a dataset of 22 mitochondrial and nuclear markers from 92% of species in the tribe to re-examine the phylogeny of...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/04/02/003749
biorxiv
by Konstantin Berlin; Sergey Koren; Chen-Shan Chin; James Drake; Jane M Landolin; Adam M Phillippy
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We report reference-grade de novo assemblies of four model organisms and the human genome from single-molecule, real-time (SMRT) sequencing. Long-read SMRT sequencing is routinely used to finish microbial genomes, but the available assembly methods have not scaled well to larger genomes. Here we introduce the MinHash Alignment Process (MHAP) for efficient overlapping of noisy, long reads using probabilistic, locality-sensitive hashing. Together with Celera Assembler, MHAP was used to...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/08/14/008003
biorxiv
by Mark D Robinson; Abdullah Kahraman; Charity W Law; Helen Lindsay; Malgorzata Nowicka; Lukas M Weber; Xiaobei Zhou
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DNA methylation, and specifically the reversible addition of methyl groups at CpG dinucleotides genome-wide, represents an important layer that is associated with the regulation of gene expression. In particular, aberrations in the methylation status have been noted across a diverse set of pathological states, including cancer. With the rapid development and uptake of large scale sequencing of short DNA fragments, there has been an explosion of data analytic methods for processing and...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/08/29/007120
biorxiv
by Roni H. G. Wright; Francois LeDily; Daniel Soronellas; Andy Pohl; Jaume Bonet; A. Silvina Nacht; Guillermo P Vicent; Michael Wierer; Baldo Oliva; Miguel Beato
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Key nuclear processes in eukaryotes including DNA replication or repair and gene regulation require extensive chromatin remodeling catalyzed by energy consuming enzymes. How the energetic demands of such processes are ensured in response to rapid stimuli remains unclear. We have analyzed this question in the context of the massive gene regulation changes induced by progestins in breast cancer cells and found that ATP is generated in the cell nucleus via the hydrolysis of poly-ADP-ribose to...
Topic: Molecular Biology
Source: http://biorxiv.org/content/early/2014/06/25/006593
biorxiv
by Endre Sebestyén; Michał Zawisza; Eduardo Eyras
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Cancer genomics has been instrumental to determine the genetic alterations that are predictive of various tumor conditions. However, the majority of these alterations occur at low frequencies, motivating the need to expand the catalogue of cancer signatures. Alternative pre-mRNA splicing alterations, which bear major importance for the understanding of cancer, have not been exhaustively studied yet in the context of recent cancer genome projects. In this article we analyze RNA sequencing data...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/07/07/006908
biorxiv
by Alexander Gusev; S Hong Lee; Benjamin M Neale; Gosia Trynka; Bjarni J Vilhjalmsson; Hilary Finucane; Han Xu; Chongzhi Zang; Stephan Ripke; Eli Stahl; n/a Schizophrenia Working Group of the PGC; n/a SWE-SCZ Consortium; Anna K Kahler; Christina M Hultman; Shaun M Purcell; Steven A McCarroll; Mark Daly; Bogdan Pasaniuc; Patrick F Sullivan; Naomi R Wray; Soumya Raychaudhuri; Alkes L Price
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Common variants implicated by genome-wide association studies (GWAS) of complex diseases are known to be enriched for coding and regulatory variants. We applied methods to partition the heritability explained by genotyped SNPs (h2g) across functional categories (while accounting for shared variance due to linkage disequilibrium) to genotype and imputed data for 11 common diseases. DNaseI Hypersensitivity Sites (DHS) from 218 cell-types, spanning 16% of the genome, explained an average of 79% of...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/04/20/004309
biorxiv
by Katarzyna Bryc; Eric Durand; J Michael Macpherson; David Reich; Joanna Mountain
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Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans brought largely by the Trans-Atlantic slave trade, shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/09/18/009340
biorxiv
by Anna-Sophie Fiston-Lavier; Maite G. Barrón; Dmitri A. Petrov; Josefa González
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Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine,...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/09/16/002964
biorxiv
by Alyssa C Frazee; Geo Pertea; Andrew E Jaffe; Ben Langmead; Steven L Salzberg; Jeffrey T Leek
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We have built a statistical package called Ballgown for estimating differential expression of genes, transcripts, or exons from RNA sequencing experiments. Ballgown is designed to work with the popular Cufflinks transcript assembly software and uses well-motivated statistical methods to provide estimates of changes in expression. It permits statistical analysis at the transcript level for a wide variety of experimental designs, allows adjustment for confounders, and handles studies with...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/09/05/003665
biorxiv
by Brendan Bulik-Sullivan; Po-Ru Loh; Hilary Finucane; Stephan Ripke; Jian Yang; Schizophrenia Working Group Psychiatric Genomics Consortium; Nick Patterson; Mark J Daly; Alkes L Price; Benjamin M Neale
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Both polygenicity (i.e. many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield inflated distributions of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from bias and true signal from polygenicity. We have developed an approach that quantifies the contributions of each by examining the relationship between test statistics and linkage disequilibrium (LD). We...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/02/21/002931
biorxiv
by Giuseppe Narzisi; Jason A O'Rawe; Ivan Iossifov; Han Fang; Yoon-ha Lee; Zihua Wang; Yiyang Wu; Gholson J Lyon; Michael Wigler; Michael C Schatz
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We present a new open-source algorithm, Scalpel, for sensitive and specific discovery of INDELs in exome-capture data. By combining the power of mapping and assembly, Scalpel carefully searches the de Bruijn graph for sequence paths that span each exon. A detailed repeat analysis coupled with a self-tuning k-mer strategy allows Scalpel to outperform other state-of-the-art approaches for INDEL discovery. We extensively compared Scalpel with a battery of >10000 simulated and >1000...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/06/18/001370
biorxiv
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Methylation of DNA is known to be essential to development and dramatically altered in cancers. The Illumina HumanMethylation450 BeadChip has been used extensively as a cost-effective way to profile nearly half a million CpG sites across the human genome. Here we present DiffVar, a novel method to test for differential variability between sample groups. DiffVar employs an empirical Bayes model framework that can take into account any experimental design and is robust to outliers. We applied...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/09/06/008847
biorxiv
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1. Understanding how landscape features affect functional connectivity among populations is a cornerstone of landscape genetic analyses. However, parameterization of resistance surfaces that best describe connectivity is largely a subjective process that explores a limited parameter space. 2. ResistanceGA is a new R package that utilizes a genetic algorithm to optimize resistance surfaces based on pairwise genetic distances and either CIRCUITSCAPE resistance distances or cost distances...
Topic: Ecology
Source: http://biorxiv.org/content/early/2014/07/29/007575
biorxiv
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Temporal dynamics in many biomolecular circuits can change with temperature because of the temperature dependence of underlying reaction rate parameters. It is generally unclear what circuit mechanisms can inherently facilitate robustness in the dynamics to variations in temperature. Here, we address this issue using a combination of mathematical models and experimental measurements in a cell-free transcription-translation system. We find that negative transcriptional feedback can reduce the...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2014/07/22/007385
biorxiv
by Chiara Barbieri; Mário Vicente; Sandra Oliveira; Koen Bostoen; Jorge Rocha; Mark Stoneking; Brigitte Pakendorf
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Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000-5000 years, reaching different parts of southern Africa 1200-2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/02/18/002808
biorxiv
by Hayan Lee; James Gurtowski; Shinjae Yoo; Shoshana Marcus; W. Richard McCombie; Michael Schatz
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Third generation single molecule sequencing technology is poised to revolutionize genomics by enabling the sequencing of long, individual molecules of DNA and RNA. These technologies now routinely produce reads exceeding 5,000 basepairs, and can achieve reads as long as 50,000 basepairs. Here we evaluate the limits of single molecule sequencing by assessing the impact of long read sequencing in the assembly of the human genome and 25 other important genomes across the tree of life. From this,...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/06/18/006395
biorxiv
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The development of CRISPR/Cas9 technologies promises a quantum leap in genome-engineering of model organisms. However, CRISPR-mediated gene targeting reports in Drosophila are still restricted to a few genes, use variable experimental conditions and vary in efficiency, questioning the universal applicability of the method. Here, we developed an efficient, two-step strategy to flexibly engineer the fly genome by combining CRISPR with recombinase-mediated cassette exchange (RMCE). In the first...
Topic: Developmental Biology
Source: http://biorxiv.org/content/early/2014/08/11/007864
biorxiv
by Maria-Ines Fariello; Bertrand Servin; Gwenola Tosser-Klopp; Rachelle Rupp; Carole Moreno; International Sheep Genomics Consortium n.a.; Magali San Cristobal; simon boitard
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The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/04/11/001453
biorxiv
by Christoph Lippert; Francesco Paolo Casale; Barbara Rakitsch; Oliver Stegle
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Multi-trait mixed models have emerged as a promising approach for joint analyses of multiple traits. In principle, the mixed model framework is remarkably general. However, current methods implement only a very specific range of tasks to optimize the necessary computations. Here, we present a multi-trait modeling framework that is versatile and fast: LIMIX enables to flexibly adapt mixed models for a broad range of applications with different observed and hidden covariates, and variable study...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/05/22/003905
biorxiv
by Önder Kartal; Oliver Ebenhöh; Martin Steup
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Carbohydrate polymers are ubiquitous in biological systems and their roles are highly diverse, ranging from energy storage over mechanical stabilisation to mediating cell-cell or cell-protein interactions. The functional diversity is mirrored by a chemical diversity that results from the high flexibility of how different sugar monomers can be arranged into linear, branched or cyclic polymeric structures. Mathematical models describing biochemical processes on polymers are faced with various...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2014/09/01/008615
biorxiv
by Mathieu Larocque; Thierry Chénard; Rafael Najmanovich
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Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. We present i MLTC804cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. i MLTC804cdf contains 804 genes, 705 metabolites and 766 metabolic, 145 exchange and 118 transport reactions. i MLTC804cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2014/07/25/006932
biorxiv
by Matthew Maurano; Hao Wang; Sam John; Anthony Shafer; Theresa Canfield; Kristen Lee; John A Stamatoyannopoulos
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The nuclear genome of every cell harbors millions of unoccupied transcription factor (TF) recognition sequences that harbor methylated cytosines. Although DNA methylation is commonly invoked as a repressive mechanism, the extent to which it actively silences specific TF occupancy sites is unknown. To define the role of DNA methylation in modulating TF binding, we quantified the effect of DNA methyltransferase abrogation on the occupancy patterns of a ubiquitous TF capable of autonomous binding...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/02/27/003061
biorxiv
by Patrick Deelen; Daria Zhernakova; Mark de Haan; Marijke van der Sijde; Marc Jan Bonder; Juha Karjalainen; K. Joeri van der Velde; Kristin M. Abbott; Jingyuan Fu; Cisca Wijmenga; Richard J. Sinke; Morris A. Swertz; Lude Franke
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Given increasing numbers of RNA-seq samples in the public domain, we studied to what extent expression quantitative trait loci (eQTLs) and allele-specific expression (ASE) can be identified in public RNA-seq data while also deriving the genotypes from the RNA-seq reads. 4,978 human RNA-seq runs, representing many different tissues and cell-types, passed quality control. Even though this data originated from many different laboratories, samples reflecting the same cell-type clustered together,...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/08/01/007633
biorxiv
by Baohu Ji; Kerin Higa; Minjung Kim; Lynn Zhou; Jared Young; Mark Geyer; Xianjin Zhou
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The t(1; 11) translocation appears to be the causal genetic lesion with 70% penetrance for schizophrenia, major depression, and other psychiatric disorders in a Scottish family. Molecular studies identified the disruption of the DISC1 (disrupted-in-schizophrenia 1) gene by chromosome translocation at chromosome 1q42. Our previous studies, however, revealed that the translocation also disrupted another gene, Boymaw (also termed DISC1FP1), on chromosome 11. After translocation, two fusion genes...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/31/005710
biorxiv
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Abstract: Discovery of novel natural products is an accepted method for the elucidation of pharmacologically active molecules and drug leads. Best known sources for such discovery have been terrestrial plants and microbes, accounting for about 85% of the approved natural products in pharmaceutical use (1), and about 60% of approved pharmaceuticals and new drug applications annually (2). Discovery in the marine environment has lagged due to the difficulty of exploration in this ecological niche....
Topic: Pharmacology
Source: http://biorxiv.org/content/early/2014/05/24/005454
biorxiv
by Gonçalo Lopes; Niccolò Bonacchi; João Frazão; Joana Neto; Bassam Atallah; Sofia Soares; Luís Moreira; Sara Matias; Pavel M. Itskov; Patrícia Correia; Roberto Medina; Elena Dreosti; Joseph J. Paton; Adam R. Kampff
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The design of modern scientific experiments requires the control and monitoring of many parallel data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for processing data streams. We will describe Bonsai's core principles and architecture while specifically...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/07/02/006791
biorxiv
by Alex Gomez-Marin; Joseph J Paton; Adam R Kampff; Rui M Costa; Zachary M Mainen
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Behavior is a unifying organismal process where genes, neural function, anatomy and environment converge and interrelate. Here we review the current state and discuss the future impact of accelerating advances in technology for behavioral studies, focusing on rodents as an exemplar. We frame our perspective in three dimensions: degree of experimental constraint, dimensionality of data, and level of description. We argue that "big behavioral data" presents challenges proportionate to...
Topic: Animal Behavior and Cognition
Source: http://biorxiv.org/content/early/2014/07/17/006809
biorxiv
by François Le Dily; Davide Baù; Andy Pohl; Guillermo P. Vicent; Daniel Soronellas; Giancarlo Castellano; François Serra; Roni H. G. Wright; Cecilia J. Ballare; Guillaume Filion; Marc A. Marti-Renom; Miguel Beato
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The human genome is segmented into Topologically Associating Domains (TADs), but the role of this conserved organization during transient changes in gene expression is not known. Here we described the distribution of Progestin-induced chromatin modifications and changes in transcriptional activity over TADs in T47D breast cancer cells. Using ChIP-Seq, Hi-C and 3D modelling techniques, we found that the borders of the ~2,000 TADs in these cells are largely maintained after hormone treatment but...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/03/13/003293
biorxiv
by Victoria Hsiao; Emmanuel LC de los Santos; Weston R Whitaker; John E Dueber; Richard M Murray
movies
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As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we de- sign, model, and implement a biomolecular concentration tracker, in which an output protein tracks the concentration of an input protein. Using synthetic scaffolds built from small, mod- ular protein-protein...
Topic: Synthetic Biology
Source: http://biorxiv.org/content/early/2013/12/10/000448
biorxiv
by Taylor Jensen; Sung K Kim; Zhanyang Zhu; Christine Chin; Claudia Gebhard; Tim Lu; Cosmin Deciu; Dirk van den Boom; Mathias Ehrich
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Background Circulating cell free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the genetically distinct maternal and fetal DNA. Current testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA and thus support additional clinical opportunities; however, this depends on knowledge of the methylomes of ccf DNA and its cellular contributors. Results Whole genome...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/04/11/004101
biorxiv
by John Aach; Prashant Mali; George M Church
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CRISPR/Cas9 systems enable many molecular activities to be efficiently directed in vivo to user-specifiable DNA sequences of interest, including generation of dsDNA cuts and nicks, transcriptional activation and repression, and fluorescence. CRISPR targeting relies on base pairing of short RNA transcripts with their target DNA sequences that must also be adjacent to fixed DNA motifs. However, rules for Cas9 targeting specificity are incompletely known. With increasing numbers of Cas9 systems...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/05/12/005074
biorxiv
by Jingqun Ao; Yinnan Mu; Li-Xin Xiang; DingDing Fan; MingJi Feng; Shicui Zhang; Qiong Shi; Lv-Yun Zhu; Ting Li; Yang Ding; Li Nie; Qiuhua Li; Wei-ren Dong; Liang Jiang; Bing Sun; XinHui Zhang; Mingyu Li; Hai-Qi Zhang; ShangBo Xie; YaBing Zhu; XuanTing Jiang; Xianhui Wang; Pengfei Mu; Wei Chen; Zhen Yue; Zhuo Wang; Jun Wang; Jian-Zhong Shao; Xinhua Chen
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The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/08/18/008136
biorxiv
by Kathleen M Fisch; Tobias Meißner; Louis Gioia; Jean-Christophe Ducom; Tristan Carland; Salvatore Loguercio; Andrew I. Su
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Omics Pipe (https://bitbucket.org/sulab/omics_pipe) is a computational platform that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas. Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis.
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/08/23/008383
biorxiv
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Restriction-site associated genomic markers are a powerful tool for investigating evolutionary questions at the population level, but are limited in their utility at deeper phylogenetic scales where fewer orthologous loci are typically recovered across disparate taxa. While this limitation stems in part from mutations to restriction recognition sites that disrupt data generation, an alternative source of data loss comes from the failure to identify homology during bioinformatic analyses....
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2013/12/03/001081
biorxiv
by Andre M Bastos; Julien Vezoli; Conrado A Bosman; Jan-Mathijs Schoffelen; Robert Oostenveld; Jarrod R Dowdall; Peter De Weerd; Henry Kennedy; Pascal Fries
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Visual cortical areas are thought to form a hierarchy and to subserve cognitive functions by interacting in both feedforward and feedback directions. While feedforward influences convey sensory signals, feedback influences modulate brain responses to a given sensory stimulus according to the current behavioural context. Many studies have demonstrated effects of feedback influences on feedforward driven responses and on behaviour. Also, anatomical projections in both directions have been...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/06/004804
biorxiv
by Johannes Kohl; Julian Ng; Sebastian Cachero; Michael-John Dolan; Ben Sutcliffe; Daniel Krüger; Shahar Frechter; Gregory SXE Jefferis
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Genetically encoded fluorescent proteins and immunostainings are widely used to detect cellular or sub-cellular structures in thick biological samples. However, each approach suffers from limitations, including low signal and limited spectral flexibility or slow speed, poor penetration and high background, respectively. Here we overcome these limitations by using transgenically expressed chemical tags for rapid, even and low-background labeling of thick biological tissues. We construct a...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/19/005298
biorxiv
by Po-Ru Loh; George Tucker; Brendan K Bulik-Sullivan; Bjarni J Vilhjalmsson; Hilary K Finucane; Daniel I Chasman; Paul M Ridker; Benjamin M Neale; Bonnie Berger; Nick Patterson; Alkes L Price
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Linear mixed models are a powerful statistical tool for identifying genetic associations and avoiding confounding. However, existing methods are computationally intractable in large cohorts, and may not optimize power. All existing methods require time cost O(MN^2) (where N = #samples and M = #SNPs) and implicitly assume an infinitesimal genetic architecture in which effect sizes are normally distributed, which can limit power. Here, we present a far more efficient mixed model association...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/08/09/007799
biorxiv
by David Lovell; Vera Pawlowsky-Glahn; Juan José Egozcue; Samuel Marguerat; Jürg Bähler
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In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative\---|or compositional\---|data, differential expression needs careful interpretation, and correlation\---|a statistical workhorse for analyzing pairwise relationships\---|is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data. We...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/08/25/008417
biorxiv
by Kimberly F. McManus; Joanna L. Kelley; Shiya Song; Krishna Veeramah; August E. Woerner; Laurie S. Stevison; Oliver A. Ryder; Great Ape Genome Project; Jeffrey M. Kidd; Jeffrey D. Wall; Carlos D. Bustamante; Michael F. Hammer
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While population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole genome sequences from 14 western...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/09/16/009191
biorxiv
by Anil Raj; Matthew Stephens; Jonathan K Pritchard
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Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem,...
Topic: Genetics
Source: http://biorxiv.org/content/early/2013/12/02/001073
biorxiv
by Dorit Avni; Harmen P. Hendriksma; Arnon Dag; Zehava Uni; Sharoni Shafir
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Pollen is the main protein and lipid source for honey bees (Apis mellifera), and nutritionally impoverished landscapes pose a threat to colony development. To determine colony nutritional demands, we analyzed a yearly cycle of bee-collected pollen from colonies in the field and compared it to colony worker production and honey bee body composition, for the first time in social insects. We monitored monthly bee production in ten colonies at each of seven sites throughout Israel, and trapped...
Topic: Ecology
Source: http://biorxiv.org/content/early/2014/08/28/008524
biorxiv
by Nuno A. Fonseca; Robert Petryszak; John Marioni; Alvis Brazma
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RNA-sequencing (RNA-Seq) has become the technology of choice for whole-transcriptome profiling. However, processing the millions of sequence reads generated requires considerable bioinformatics skills and computational resources. At each step of the processing pipeline many tools are available, each with specific advantages and disadvantages. While using a specific combination of tools might be desirable, integrating the different tools can be time consuming, often due to specificities in the...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/06/06/005991
biorxiv
by Andrea Ganna; Tove Fall; Woojoo Lee; Corey D Broeckling; Jitender Kumar; Sara Hägg; Patrik K.E. Magnusson; Jessica Prenni; Lars Lind; Yudi Pawitan; Erik Ingelsson
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Metabolomic profiling is an emerging technique in life sciences. Human studies using these techniques have been performed in a small number of individuals or have been targeted at a restricted number of metabolites. In this article, we propose a data analysis workflow to perform non-targeted metabolomic profiling in large human population-based studies using ultra performance liquid chromatography-mass spectrometry (UPLC-MS). We describe challenges and propose solutions for quality control,...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/02/19/002782
biorxiv
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Background The identification of apparently conserved gene complements in the venom and salivary glands of a diverse set of reptiles led to the development of the Toxicofera hypothesis the idea that there was a single, early evolution of the venom system in reptiles. However, this hypothesis is based largely on relatively small scale EST-based studies of only venom or salivary glands and toxic effects have been assigned to only some of these putative Toxcoferan toxins in some species. We set...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/06/06/006031
biorxiv
by Rajiv C McCoy; Ryan W Taylor; Timothy A Blauwkamp; Joanna L Kelley; Michael Kertesz; Dmitry Pushkarev; Dmitri A Petrov; Anna-Sophie Fiston-Lavier
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High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or present in complex genomic arrangements. While TEs...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/06/17/001834
biorxiv
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The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC)...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/05/23/005348
biorxiv
by Gosia Trynka; Harm-Jan Westra; Kamil Slowikowski; Xinli Hu; Han Xu; Barbara E Stranger; Buhm Han; Soumya Raychaudhuri
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Identifying genomic annotations that differentiate causal from associated variants is critical to fine-map disease loci. While many studies have identified non-coding annotations overlapping disease variants, these annotations colocalize, complicating fine-mapping efforts. We demonstrate that conventional enrichment tests are inflated and cannot distinguish causal effects from colocalizing annotations. We developed a sensitive and specific statistical approach that is able to identify...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/09/18/009258
biorxiv
by Alejandro Reyes; Carolin Blume; Vicent Pelechano; Petra Jakob; Lars M Steinmetz; Thorsten Zenz; Wolfgang Huber
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Background: Genome sequencing studies of chronic lympoid leukemia (CLL) have provided a comprehensive overview of recurrent somatic mutations in coding genes. One of the most intriguing discoveries has been the prevalence of mutations in the HEAT-repeat domain of the splicing factor SF3B1. A frequently observed variant is predicted to cause the substitution of a lysine with a glutamic acid at position 700 of the protein (K700E). However, the molecular consequences of the mutations are largely...
Topic: Cancer Biology
Source: http://biorxiv.org/content/early/2014/07/13/000992
biorxiv
by Jonathan Rodenfels; Oksana Lavrynenko; Sophie Ayciriex; Julio L Sampaio; Andrej Shevchenko; Suzanne Eaton
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In Drosophila larvae, growth and developmental timing are regulated by nutrition in a tightly coordinated fashion. The networks that couple these processes are far from understood. Here, we show that the intestine responds to nutrient availability by regulating production of a circulating lipoprotein-associated form of the signaling protein Hedgehog (Hh). Levels of circulating Hh tune the rates of growth and developmental timing in a coordinated fashion. Circulating Hh signals to the fat body...
Topic: Developmental Biology
Source: http://biorxiv.org/content/early/2014/07/29/002626
biorxiv
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In tropical forests, one of the most common relationships between parasites and insects is that between the fungus Ophiocordyceps (Ophiocordycipitaceae, Hypocreales, Ascomycota) and ants, especially within the tribe Camponotini. These fungi have the ability to penetrate the exoskeleton of the ant and to manipulate the behavior of the host, making it leave the nest and ascend understorey shrubs, to die biting onto the vegetation: hence, the term zombie-ant fungi to describe this behavioral...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/06/03/003806
biorxiv
by Daniele Ramazzotti; Giulio Caravagna; Loes Olde Loohuis; Alex Graudenzi; Ilya Korsunsky; Giancarlo Mauri; Marco Antoniotti; Bud Mishra
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A tumor is thought to result from successive accumulation of genetic alterations–each resulting population manifesting itself with a novel 'cancer phenotype.' In each such population, clones of higher fitness, contributing to the selection of the cancer phenotype, enjoy a Darwinian selective advantage, thus driving inexorably the tumor progression to metastasis: from abnormal growth, oncogenesis, primary tumors, to metastasis. Evading glutamine deregulation, anoxia/hypoxia, senescence,...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/08/19/008110
biorxiv
by Anil Korkut; Weiqing Wang; Emek Demir; B?lent Arman Aksoy; Xiaohong Jing; Evan Molinelli; ?zg?n Babur; Debra Bemis; David B Solit; Christine Pratilas; Chris Sander
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Systematic prediction of cellular response to perturbations is a central challenge in biology, both for mechanistic explanations and for the design of effective therapeutic interventions. We addressed this challenge using a computational/experimental method, termed perturbation biology, which combines high-throughput (phospho)proteomic and phenotypic response profiles to targeted perturbations, prior information from signaling databases and network inference algorithms from statistical physics....
Topic: Cancer Biology
Source: http://biorxiv.org/content/early/2014/09/11/008201
biorxiv
by Jean-Philippe Fortin; Aurelie Labbe; Mathieu Lemire; Brent W. Zanke; Thomas J. Hudson; Elana J. Fertig; Celia M.T. Greenwood; Kasper D. Hansen
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We propose an extension to quantile normalization which removes unwanted technical variation using control probes. We adapt our algorithm, functional normalization, to the Illumina 450k methylation array and address the open problem of normalizing methylation data with global epigenetic changes, such as human cancers. Using datasets from The Cancer Genome Atlas and a large case-control study, we show that our algorithm outperforms all existing normalization methods with respect to replication...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/02/23/002956
In the recent paper by Kim et al. (Genome biology, 2013. 14(4): p. R36) the accuracy of TopHat2 was compared to other RNA-seq aligners. In this comment we re-examine most important analyses from this paper and identify several deficiencies that significantly diminished performance of some of the aligners, including incorrect choice of mapping parameters, unfair comparison metrics, and unrealistic simulated data. Using STAR (Dobin et al., Bioinformatics, 2013. 29(1): p. 15-21) as an exemplar, we...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2013/11/22/000851
biorxiv
by Russell B. Corbett-Detig; Daniel L. Hartl; Timothy B. Sackton
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The range of genetic diversity observed within natural populations is much more narrow than expected based on models of neutral molecular evolution. Although the increased efficacy of natural selection in larger populations has been invoked to explain this paradox, to date no tests of this hypothesis have been conducted. Here, we present an analysis of whole-genome polymorphism data and genetic maps from 39 species to estimate for each species the reduction in genetic variation attributable to...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/06/09/006122
biorxiv
by Haijun Liu; Xiaqing Wang; Marilyn Warburton; Weiwei Wen; Minliang Jin; Min Deng; Jie Liu; Hao Tong; Qingchun Pan; Xiaohong Yang; Jianbing Yan
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The temperate-tropical division of early maize germplasm to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from the genomic, transcriptomic and phenotypic variation collected from 368 diverse temperate and tropical maize inbred lines in this study. This is the first attempt to systematically explore the...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/06/03/005751
biorxiv
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The t(1,11) chromosome translocation co-segregates with major psychiatric disorders in a large Scottish family. The translocation disrupts the DISC1and Boymaw (DISC1FP1) genes on chromosomes 1 and 11, respectively. After translocation, two fusion genes are generated. Our recent studies found that the DISC1-Boymaw fusion protein is localized in mitochondria and inhibits oxidoreductase activity, rRNA expression, and protein translation. Mice carrying the DISC1-Boymaw fusion genes display...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/31/005728
biorxiv
by Ophelia S Venturelli; Ignacio Zuleta; Richard M Murray; Hana El-Samad
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Delineating the strategies by which cells contend with combinatorial changing environments is crucial for understanding cellular regulatory organization. When presented with two carbon sources, microorganisms first consume the carbon substrate that supports the highest growth rate (e.g. glucose) and then switch to the secondary carbon source (e.g. galactose), a paradigm known as the Monod model. Sequential sugar utilization has been attributed to transcriptional repression of the secondary...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2014/02/21/002907
biorxiv
by James K Bonfield
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Motivation: The reference CRAM file format implementation is in Java. We present "Scramble": a new C implementation of SAM, BAM and CRAM file I/O. Results: The C API for CRAM is 1.5-1.7x slower than BAM at decoding, but 1.8-2.6x faster at encoding. We see file size savings of 40-50%. Availability: Source code is available from http://sourceforge.net/projects/staden/files/io lib/ Contact: jkb@sanger.ac.uk
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/03/28/003640